Education's goal is to teach you something so that you can then go on without them, thus why they teach a wider range of topics within a subject.
Indoctrination's goal is to make you dependent on the educator, thus why they focus on only their version of the subject and squash differing opinions using propaganda tactics.
For example, you don't have to go back to your highschool math teacher to use Algebra or back to your grade school to read something. You are independent and may never set foot in your school ever again, but can still do these things.
If you teach someone that Python is the one true language and use propaganda to make them want to use it, then they'll be dependent on that language and the community in order to write code. Even simpler is if you only teach them git and github then you've indoctrinated them into always needing github to share code.
Bad kinds of education are like History classes that teach fairy tales like "George Washington never told a lie." These are indoctrination masquerading as education because they make the student dependent on the country for their identity.
The reason indoctrination like this is bad in programming though is because programming languages and tools die all the time, and when they do it destroys these people the indoctrinators have made dependent on the technologies. It also smacks of a con that's covering for shit technology that can't survive on its own merits.
Finally, finding a particular topic in the gray area between them does not disprove that there's a difference. Rational people don't think in binary, so this is a continuum where you could find some topics that require a bit of indoctrination, and some where it's the complete wrong approach. In my opinion, programming education only has indoctrination because that lets shitty technology hide behind propaganda.
Zed is specifically referring to this usage. You should never assume you are doing the Right Thing in programming, because you probably aren't, at best you're doing the "least wrong" thing for your situation.